2113f4ab5376a69e9169e34db99d99a6ce20f8d5
hiram
  Fri Mar 25 12:05:18 2022 -0700
better name for refSeq variable refs #29111

diff --git src/hg/utils/automation/asmHubChromAlias.pl src/hg/utils/automation/asmHubChromAlias.pl
index e9d632a..798f776 100755
--- src/hg/utils/automation/asmHubChromAlias.pl
+++ src/hg/utils/automation/asmHubChromAlias.pl
@@ -112,74 +112,74 @@
   my $hashPtr = $aliasOut{$source};
   # already done, verify it is equivalent to previous request
   if (defined($hashPtr->{$alias})) {
      if ($sequence ne $hashPtr->{$alias}) {
         printf STDERR "ERROR: additional alias '%s:%s' does not match previous '%s'\n", $alias, $sequence, $hashPtr->{$alias};
         exit 255;
      }
      return;
   }
   $hashPtr->{$alias} = $sequence;
   return;
 }
 
 # asmSource - is this a genbank or refseq assembly
 my $asmSource = "genbank";
-my $refSeq = 0; #       == 0 for Genbank assembly, == 1 for RefSeq assembly
+my $isRefSeq = 0; #       == 0 for Genbank assembly, == 1 for RefSeq assembly
 if ($asmId =~ m/^GCF/) {
 #  printf STDERR "# processing a RefSeq assembly\n";
-  $refSeq = 1;
+  $isRefSeq = 1;
   $asmSource = "refseq";
 } else {
 #  printf STDERR "# processing a GenBank assembly\n";
 }
 
 my $twoBit = "../../$asmId.2bit";
 
 open (FH, "twoBitInfo $twoBit stdout|") or die "can not twoBitInfo $twoBit stdout";
 while (my $line = <FH>) {
   chomp $line;
   my ($name, $size) = split('\s+', $line);
   $sequenceSizes{$name} = $size;
   ++$sequenceCount;
 }
 
 close (FH);
 # printf STDERR "# counted %d sequence names in the twoBit file\n", $sequenceCount;
 
 my $nameCount = 0;
 my %ncbiToUcsc;	# key is NCBI sequence name, value is 'chr' UCSC chromosome name
 my %ucscToNcbi;	# key is 'chr' UCSC name, value is NCBI sequence name
 open (FH, "cat ../../sequence/*.names|") or die "can not cat ../../sequence/*.names";
 while (my $line = <FH>) {
   chomp $line;
   my ($ucscName, $seqName) = split('\s+', $line);
   $ncbiToUcsc{$seqName} = $ucscName;
   $ucscToNcbi{$ucscName} = $seqName;
   ++$nameCount;
   $ucscNames = 1 if (defined($sequenceSizes{$ucscName}));
-  if ($refSeq) {
+  if ($isRefSeq) {
     $ucscToRefSeq{$ucscName} = $seqName;
   } else {
     $ucscToGenbank{$ucscName} = $seqName;
   }
 }
 close (FH);
 
 # when not a UCSC named assembly, add the UCSC names as aliases
 if (! $ucscNames) {
-  if ($refSeq) {
+  if ($isRefSeq) {
     foreach my $ucscName (sort keys %ucscToRefSeq) {
        addAlias("ucsc", $ucscName, $ucscToRefSeq{$ucscName});
     }
   } else {
     foreach my $ucscName (sort keys %ucscToGenbank) {
        addAlias("ucsc", $ucscName, $ucscToGenbank{$ucscName});
     }
   }
 }
 
 my $dupsNotFound = 0;
 my $dupsList = "../../download/$asmId.dups.txt.gz";
 if ( -s "$dupsList" ) {
   open (FH, "zcat $dupsList | awk '{print \$1, \$3}'|") or die "can not read $dupsList";
   while (my $line = <FH>) {
@@ -262,57 +262,57 @@
 
 my $dbgCount = 0;
 # printf STDERR "# third set processing assembly_report\n";
 # column 1 is the 'assembly' name
 # column 5 is the GenBank-Accn, column 7 is the RefSeq-Accn
 open (FH, "grep -v '^#' ../../download/${asmId}_assembly_report.txt | cut -d\$'\t' -f1,5,7|") or die "can not grep assembly_report";
 while (my $line = <FH>) {
   chomp $line;
   ++$dbgCount;
   my ($asmName, $gbkName, $refSeqName) = split('\s+', $line);
   printf STDERR "# '%s'\t'%s'\t'%s'\n", $asmName, $gbkName, $refSeqName if ($dbgCount < 5);
 #  next if ($refSeqName eq "na");	# may not be any RefSeq name
 #  next if ($gbkName eq "na");	# may not be any GenBank name
   if ($refSeqName ne "na") {
     my $seqName = $refSeqName;
-    if (! $refSeq) {
+    if (! $isRefSeq) {
       $seqName = $gbkName;
     }
     if ($ucscNames) {
        $seqName = $ncbiToUcsc{$seqName};
     }
     if (!defined($seqName)) {
        if (defined($aliasOut{"refseq"})) {
          if (defined($aliasOut{"refseq"}->{$refSeqName})) {
             $seqName = $aliasOut{"refseq"}->{$refSeqName};
          }
        }
     }
     if (defined($seqName)) {
       if (defined($dupToSequence{$seqName})) {
         addAlias("refseq", $refSeqName, $dupToSequence{$seqName});
         addAlias("assembly", $asmName, $dupToSequence{$seqName});
       } else {
         addAlias("refseq", $refSeqName, $seqName);
         addAlias("assembly", $asmName, $seqName);
       }
     }
   }	#	if ($refSeqName ne "na")
 
   if ($gbkName ne "na") {
     my $seqName = $gbkName;
-    if ($refSeq) {
+    if ($isRefSeq) {
       $seqName = $refSeqName;
     }
     if ($ucscNames) {
        $seqName = $ncbiToUcsc{$seqName};
     }
     if (!defined($seqName)) {
        if (defined($aliasOut{"genbank"})) {
          if (defined($aliasOut{"genbank"}->{$gbkName})) {
             $seqName = $aliasOut{"genbank"}->{$gbkName};
          }
        }
     }
     if (defined($seqName)) {
       if (defined($dupToSequence{$seqName})) {
         addAlias("genbank", $gbkName, $dupToSequence{$seqName});